f9e9d2e273
Fix no-normal bug; add HapMap sensitivity benchmarking
2015-12-22 08:29:01 -05:00
0c3c775566
Merge pull request #1248 from broadinstitute/rhl_keep_gt
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LeftAlignAndTrimVariants --splitMultiallelics keeps GT if valid
2015-12-14 12:19:49 -05:00
9c8f035780
LeftAlignAndTrimVariants --splitMultiallelics keeps GT if valid
2015-12-14 10:42:32 -05:00
4767a83d8a
Update pom versions to mark the start of GATK 3.6 development
2015-11-25 01:52:51 -05:00
9749adf22a
Merge pull request #1236 from broadinstitute/gvda_prep_M2_release_1201
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Prep MuTect2 for release
2015-11-24 20:12:57 -05:00
bf875974d1
Prep MuTect2 and ContEst for release
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Renamed M2 to MuTect2
Renamed ContaminationWalker to ContEst
Refactored related tests and usages (including in Queue scripts)
Moved M2 and ContEst + accompanying classes from private to protected
Made QSS a StandardSomaticAnnotation (new annotation group/interface) to prevent it from being sucked in with the rest of the StandardAnnotation group
2015-11-24 16:43:20 -05:00
1f8e45f0ba
Merge pull request #1243 from broadinstitute/gvda_rodwalkers_dont_downsample_1179
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Fix bug where gatkdocs of RodWalkers reported default LocusWalker downsampling settings
2015-11-23 21:39:43 -05:00
88a0514ec7
Fix bug where gatkdocs of RodWalkers reported default LocusWalker downsampling settings
2015-11-23 17:53:19 -05:00
5a3756410c
Merge pull request #1231 from broadinstitute/mf_fixBQSRIntegrationTest
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Fixes testPRWithConflictingArguments_qqAndSQQ to use -ql rather than -q1
2015-11-23 17:08:30 -05:00
b0730c2b81
Merge pull request #1239 from broadinstitute/gvda_straggler_doc_fixes_1237
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Improve doc block of GatherBqsrReports
Annotation doc enhancements (QD, InbreedingCoeff, ExcessHet and AS versions where applicable)
2015-11-22 13:58:20 -05:00
0babe6abf7
Merge pull request #1241 from broadinstitute/gvda_undeprecate_FindCoveredIntervals_1240
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Restore FindCoveredIntervals + add docs
2015-11-22 13:56:25 -05:00
a7748368f8
Yet more doc improvements prior to 3.5 release
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Improve doc block of GatherBqsrReports
Annotation doc enhancements (QD, InbreedingCoeff, ExcessHet and AS versions where applicable)
2015-11-22 10:59:24 -05:00
46ba0e519e
Restore FindCoveredIntervals + add docs
2015-11-22 10:19:04 -05:00
8f0ce02838
Merge pull request #1233 from broadinstitute/rhl_fix_example_bcf_dict
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Make the BAM header sequence dictionary match reference
2015-11-21 21:45:16 -05:00
08a9c80559
Make the header sequence dictionary match reference
2015-11-21 19:12:37 -05:00
22fa1511be
Merge pull request #1235 from broadinstitute/gvda_deprecate_useless_tools_1192
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Deprecate tools that were outdated or redundant
2015-11-21 14:58:00 -05:00
592d43f3b3
Merge pull request #1209 from broadinstitute/gvda_yet_more_doc_fixes_1195
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Many doc improvements and typo fixes
2015-11-21 02:26:46 -05:00
1cf66addaa
Deprecate tools that were outdated or redundant
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ReadAdaptorTrimmer (unsound and untested)
BaseCoverageDistribution (redundant with DiagnoseTargets)
CoveredByNSamplesSites (redundant with DiagnoseTargets)
FindCoveredIntervals (redundant with DiagnoseTargets)
VariantValidationAssessor (has a scary TODO -- REWRITE THIS TO WORK WITH VARIANT CONTEXT comment and zero tests)
LiftOverVariants, FilterLiftedVariants and liftOverVCF.pl (in #1106 ) (use Picard liftover tool)
sortByRef.pl (use Picard SortVCF)
ListAnnotations (useless)
Also deleted the java archive from the private repository (old junk we never use)
2015-11-20 22:49:40 -05:00
2570cab24c
Assorted documentation fixes, enhancements and reorganization.
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See issues referenced by the pull request for details.
2015-11-20 22:44:46 -05:00
6722ac8e8a
Merge pull request #1230 from broadinstitute/rhl_htsjdk_picard_1.141
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Rhl htsjdk picard 1.141
2015-11-20 19:47:54 -05:00
0b3b09e3ff
Move htsjdk & picard to version 1.141
2015-11-20 16:26:26 -05:00
dc0e32e3aa
Merge pull request #1223 from broadinstitute/rhl_dict_check
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Validate VCF with sequence dictionary
2015-11-20 12:43:44 -05:00
1443ee8c7f
Fixes testPRWithConflictingArguments_qqAndSQQ to use -ql rather than -q1
2015-11-20 11:23:02 -05:00
ccaddefa19
Validate VCF with sequence dictionary
2015-11-20 09:23:24 -05:00
29e86a0d01
Merge pull request #1222 from broadinstitute/yf_percent_informative_read
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Adding fraction informative reads annotation.
2015-11-18 10:08:50 -05:00
4da0d1300c
adding fraction informative reads annotation.
2015-11-18 08:39:47 -05:00
2bffe0b428
Merge pull request #1219 from broadinstitute/dr_move_GatherBqsrReports_to_protected
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Move GatherBqsrReports from private to protected
2015-11-16 22:26:54 -05:00
9d5be24778
Move GatherBqsrReports from private to protected
2015-11-10 17:40:58 -05:00
2b591d0b6f
Merge pull request #1198 from broadinstitute/ldg_moreASannotations
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Allele-specific QD and InbreedingCoeff
2015-11-10 00:35:15 -05:00
25b8ba45f4
More allele-specific annotations: AS_QD and AS_InbreedingCoeff
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Grouped default output annotations to keep them from getting dropped when -A is specified; addresses #918
Also refactored code shared by ExcessHet and InbreedingCoeff
2015-11-09 16:38:31 -05:00
fa6c1c933b
Merge pull request #1193 from broadinstitute/vrr_general_independent_af_calculator
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Added the AF independent calculator for any ploidy but seems that is no…
2015-11-07 22:14:23 -05:00
e3d5d96076
Added the AF indepdent calculator for any ploidy but seems that is not doing a good job for haploid
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Addresses issue #1078 by implementing a any-ploidy version of the independent-allele-exact-ac-calculator already available for diploids.
Notice that this will change result somewhat when dealing with noisy data (low GQs).
2015-11-07 16:17:30 -05:00
49fa06865c
Merge pull request #1207 from broadinstitute/mf_SV_bugfix
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Resolves issue #1061 to use testid1 rather than testid in two integra…
2015-11-06 08:52:38 -05:00
8857bc9b3f
Resolves issue #1061 to use testid1 rather than testid in two integrationtests.
2015-11-05 22:20:20 -05:00
975f8a8502
Merge pull request #1206 from broadinstitute/eb_suppress_alt_allele_warnings
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Suppress emission of the scary warning message from genotyping to no …
2015-11-05 16:12:50 -05:00
2cc7de4886
Suppress emission of the scary warning message from genotyping to no more than once in
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anything but DEBUG logging mode. Otherwise it fills up our output logs.
2015-11-05 14:19:21 -05:00
448b575701
Merge pull request #1204 from broadinstitute/ms_fix_SelectVariants
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Fix for out of date VCF version output from SelectVariants
2015-11-05 08:07:48 -05:00
e4627ed5c3
Addressing comments
2015-11-04 11:00:01 -05:00
b5165b8d30
Fix for out of date VCF version output
2015-11-03 17:35:47 -05:00
3d1dc303b3
Merge pull request #1197 from broadinstitute/ts_ve_nullPointer
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Prevent null pointer exception in PrintMissingComp module
2015-11-02 14:42:50 -05:00
33462c7b50
Removed the line that caused a null pointer, as the information it logged was not useful. Updated docs and added an integration test to ensure the code no longer throws the exception.
2015-11-02 12:45:09 -05:00
54ab65a340
Merge pull request #1187 from broadinstitute/ldg_variantEval_famStrat
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Enable family-level stratification (if a ped file is provided)
2015-10-30 08:00:30 -04:00
f7eb5d3082
Enable family-level stratification (if a ped file is provided)
2015-10-28 09:55:04 -04:00
4fbcfc2e36
Merge pull request #1173 from broadinstitute/ldg_AS_annotations
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New map-combine-finalize annotation framework
2015-10-27 12:04:56 -04:00
84006a629b
Merge pull request #1190 from broadinstitute/mf_makeRDQHidden
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Fixed an NA12878 Knowledgebase test, and made the RDQ option for BQSR…
2015-10-27 11:59:35 -04:00
68a2f1243d
Finished draft of code for new map-combine-reduce annotation framework
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All VQSR annotations can be generated in allele-specific mode
Pull out allele-specific annotations in AS_Standard annotation group
2015-10-27 09:44:49 -04:00
19af5724c5
Fixed an NA12878 Knowledgebase test, and made the RDQ option for BQSR binning hidden
2015-10-27 09:44:26 -04:00
fcaf37279c
Finished draft of code for new map-combine-reduce annotation framework
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All VQSR annotations can be generated in allele-specific mode
Pull out allele-specific annotations in AS_Standard annotation group
2015-10-27 09:23:29 -04:00
ab247e7570
Merge pull request #1189 from broadinstitute/rhl_laatv_long_allele_choke
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Allow LeftAlignAndTrimVariants to handle alleles longer than the default processing window
2015-10-26 11:02:55 -04:00
36ca9fe898
Allow LeftAlignAndTrimVariants to handle alleles longer than the default processing window
2015-10-25 20:33:56 -04:00
Laura Gauthier
Ron Levine
Geraldine Van der Auwera
Mark Fleharty
meganshand
Mark Fleharty
Yossi Farjoun
Yossi Farjoun
Eric Banks
David Roazen
Valentin Ruano Rubio
vruano
Takuto Sato